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Detailed information for vg0909128170:

Variant ID: vg0909128170 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 9128170
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.94, A: 0.05, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:

ATGCATGGCGTTAATCCACGATTCATCAGTTAATGCATGAGTAACATCTTTGGGTACAAAAGAAGCAACAAATGCAGAATTTGCACAAACATCATGAGTC[G/A]
TTACCTTAAACATTGTAGCCCGCTCACCTATATTATCAATGATTTGTTCTCGCGGATATTGTCGTTGAATATGCAAAGTAGCAGCGACTTCTGAAGTTGT

Reverse complement sequence

ACAACTTCAGAAGTCGCTGCTACTTTGCATATTCAACGACAATATCCGCGAGAACAAATCATTGATAATATAGGTGAGCGGGCTACAATGTTTAAGGTAA[C/T]
GACTCATGATGTTTGTGCAAATTCTGCATTTGTTGCTTCTTTTGTACCCAAAGATGTTACTCATGCATTAACTGATGAATCGTGGATTAACGCCATGCAT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	55.40%	44.50%	0.13%	0.00%	NA
All Indica	2759	89.60%	10.30%	0.14%	0.00%	NA
All Japonica	1512	0.70%	99.20%	0.07%	0.00%	NA
Aus	269	33.10%	66.50%	0.37%	0.00%	NA
Indica I	595	90.10%	9.90%	0.00%	0.00%	NA
Indica II	465	96.80%	3.00%	0.22%	0.00%	NA
Indica III	913	88.40%	11.40%	0.22%	0.00%	NA
Indica Intermediate	786	86.40%	13.50%	0.13%	0.00%	NA
Temperate Japonica	767	0.40%	99.60%	0.00%	0.00%	NA
Tropical Japonica	504	0.80%	99.20%	0.00%	0.00%	NA
Japonica Intermediate	241	1.70%	97.90%	0.41%	0.00%	NA
VI/Aromatic	96	17.70%	82.30%	0.00%	0.00%	NA
Intermediate	90	30.00%	70.00%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0909128170	G -> A	LOC_Os09g15070-LOC_Os09g15090	intergenic_region ; MODIFIER	silent_mutation	Average:34.106; most accessible tissue: Minghui63 young leaf, score: 53.016	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0909128170	NA	4.93E-06	mr1029	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0909128170	NA	5.71E-10	mr1047	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0909128170	NA	4.48E-10	mr1151	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0909128170	NA	5.53E-06	mr1189	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0909128170	NA	9.66E-06	mr1734	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0909128170	NA	1.36E-07	mr1796	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0909128170	NA	1.33E-06	mr1990	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0909128170	NA	3.35E-13	mr1189_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0909128170	NA	1.37E-27	mr1323_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0909128170	NA	1.76E-08	mr1449_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0909128170	NA	1.40E-14	mr1579_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0909128170	NA	6.31E-12	mr1734_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0909128170	NA	9.29E-12	mr1782_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0909128170	NA	2.82E-09	mr1834_2	All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251